Abstract: In aircraft assembly, it is widely used to install temporary fasteners to fix the relative position between components, which is called pre-joining. This pre-joining operation can also eliminate the gap between the contact surfaces and enhance the stability of the structure. Aiming at aircraft composite panel assembly, in order to improve the pre-joining efficiency and assembly quality, an optimization method of the number and layout of temporary fasteners considering composite material damage was proposed. Combining the finite element method and genetic algorithm, this optimization method aimed at improving the elimination rate of gap between panels and frames, and reducing the number of temporary fasteners installed. In this optimization method, the number, layout and load of temporary fasteners were taken as control variables, and the damage state of the composite panel predicted by 3D Hashin criterion was taken as constraint conditions. An experimental model of pre-joining of compo-site panel was taken as an example to demonstrate that this optimization technology can avoid the damage of composite panels, and achieve a higher gap elimination rate with less temporary fasteners.